[gmx-users] genbox + python bug?

Marcelo Depólo marcelodepolo at gmail.com
Fri Mar 13 18:27:51 CET 2015


Thanks for the insights, Mark.

It was a 'aprun' issue. When I remove it from the command, everything
worked out.

--
Marcelo

2015-03-13 14:10 GMT-03:00 Mark Abraham <mark.j.abraham at gmail.com>:

> On Fri, Mar 13, 2015 at 5:46 PM, Marcelo Depólo <marcelodepolo at gmail.com>
> wrote:
>
> > Hey,
> >
> > I have a python script running gmx commands (version 4.6.7) until the
> > following:
> >
> >
> >
> > *if systype == 'system_1' or systype == 'system_2':    genboxcommand =
> > "aprun -n 1 genbox_mpi -cs spc216.gro -cp " + prefix + ".min0.gro -p " +
> > prefix + ".top -o " + prefix + ".wat.gro -maxsol " + str(water+ion) + ""
> > os.system(genboxcommand)*
> >
> > And I get the following:
> >
> >
> > *Invalid command line argument:--cp*
> >
> > As you can see, the -cp flag is correct at the command, but inside the
> > script it is read as '--cp' for some reason. Also, other gmx commands run
> > just fine before the crash. This might be a synergetic bug from python
> and
> > genbox?
> >
> > Does anyone has a suggestion?
> >
>
> I'd actually suspect aprun of over-stepping its bounds - I seem to recall
> some issue like this reported. Anyway, it is useless to run genbox with MPI
> (and generally useless to do so in a workflow that needs to run mdrun on a
> machine where aprun would be used, where your compute resources are lying
> idle while genbox and friends do string processing and file I/O...), so I'd
> either do my non-mdrun processing separately, or via a version of GROMACS
> that is not compiled to run with MPI. Perhaps you can get away with just
> running genbox_mpi on its own, YMMV.
>
> Mark
>
>
> > --
> > Marcelo Depólo Polêto
> > B.Sc. Biochemistry - University of Viçosa (Brazil)
> > --
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-- 
Marcelo Depólo Polêto
B.Sc. Biochemistry - University of Viçosa (Brazil)


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